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Center for Clinical and Translational Science

Tools and Services

  • Build a UAB Cohort with i2b2

    Informatics for Integrating Biology & the Bedside

    i2b2 is a self-service 'cohort discovery tool' available to all personnel. It allows you to explore and query clinical data that has been deidentified and aggregated. i2b2 allows you to count patients with specific characteristics and services, as well as to save cohorts.

    Login to i2b2

    Need assistance? researchdata@uabmc.edu

    Click here for information on types of data available in i2b2.

    Office Hours with i2b2 Training
    i2b2_Manual.pdf
    i2b2_FAQ.pdf
    UAB i2b2 Training Videos

  • Cohort Analytics

    Statistics on any Cohorts saved in i2b2

    The DataLENS Application includes Self-Service Cohort Analysis for patient sets created in i2b2, in which frequencies and comparison to overall UAB populations is possible for various data domains, including Demographics, Encounters, Procedures, etc.

    View Cohort Work List

    Need assistance?researchdata@uabmc.edu

    The current list of data domains includes Demographics and Encounters, but Procedures, Labs, Medications and others are coming soon.

    To use the Cohort Analytics, select a Cohort from your Work List, then choose 'Analytics' in the horizontal sub menu.

  • Documentation and Storage

    UAB File Share, Box.com and others

    Services are available for organizing and sharing documents, such as standard operating procedures (SOP), data management and analysis protocols, reports, grant proposals, manuscripts, and other important files related to R&D processes in a modern research team.

    Login to UAB Box

    Need assistance? researchdata@uabmc.edu

    UAB supports multiple solutions for document storage for all types of data classifications. See the UAB Classification System for details on storage solutions that fit your needs.

    For a full list of storage systems supported by UAB, please visit UAB Storage Options.

  • Re-usable Pipelines

    Omics Processing and Demos

    Various re-usable data processing pipelines are available for an assortment of purposes.

    Request Help via Email

    Need assistance?researchdata@uabmc.edu

    QWRAP microbiome data analysis pipeline: Read the QWRAP Paper or browse other pipelines and templates from CCTS Informatics at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines (Login required).

    AGHIpop GWAS pipeline for analyzing data from the Alabama Genomic Health Initiative: Visit https://ubrite.org/aghi/.

    Single cell RNAseq data analysis tutorial from Dr. Min Gao: Source code and workshop slides at https://zenodo.org/records/3700066.

    Hackathon projects, example notebooks, technology demos: Visit the Gitlab page here: https://gitlab.rc.uab.edu/U-BRITE

  • Screening or Chart Abstraction Tools

    Phedrs and IMPACT Access
    Phedrs: Chart review capability can be provided for population screening for enrollment or cohort inclusion, or for detailed data collection or abstraction for Analysis. IMPACT access for an IRB Protocol allows full, read only access to the EHR.

    Request Access via Email

    Need assistance?researchdata@uabmc.edu Chart review capability can be provided for population screening for enrollment or cohort inclusion, or for detailed data collection or abstraction for Analysis.

    Daily/Weekly detected patients can be loaded to a PheDRS Registry for review and determination by the Study Team.

    - The Registry view provides Demographics, visits, labs, meds, and documents - PHI, or De-Identified

  • Source Code Management

    Gitlab hosted by Research Computing

    We help connect research teams to git-based IT infrastructure, training in modern practices, and tooling for interacting with the extensive git ecosystem.

    Click below to login to RC Gitlab.

    Login to RC Gitlab

    Need assistance?researchdata@uabmc.edu

    The Source Code Repository is for version control of source code and other research artifacts to better facilitate team science and reproducible research. In particular, we help connect research teams to git-based IT infrastructure, training in modern practices, and tooling for interacting with the extensive git ecosystem. This encourages and enables the participation of the entire team, not just a handful of investigators, in the R&D process and promotes sharing of web notebooks, pipelines, and other research products within and among research teams. Currently, the Source Code Repository is implemented on a UAB-local instance of GitLab, maintained and supported by Research Computing.

  • UAB De-Identified Datasets

    Dataset Builder in DataLENS

    The DataLENS Application includes a Standard Dataset Builder, which allows the creation of detailed clinical datasets in De-Identified (HIPAA Limited Dataset) form. The cohorts, and datasets are controlled and track such that they fall within IRB Exempts requirements.

    Standard Dataset Bulder

    Need assistance? researchdata@uabmc.edu

    Click here for information on types of data available for the Standard Dataset Builder.

    Training Resources Coming Soon

  • UAB Medicine ShareFile

    Share files with PHI

    ShareFile offers the ability for exchange of PHI or other sensitive data when access outside of the DataLENS application is required. Assistance from developers is available.

    Request Help via Email

    Need assistance? researchdata@uabmc.edu